Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography
Jazyk angličtina Země Velká Británie, Anglie Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
ANR-10-INBS-0005-02
Agence Nationale de la Recherche (French National Research Agency)
ANR-17-EURE-0003
Agence Nationale de la Recherche (French National Research Agency)
PubMed
38355696
PubMed Central
PMC10867305
DOI
10.1038/s41467-024-45770-6
PII: 10.1038/s41467-024-45770-6
Knihovny.cz E-zdroje
- MeSH
- Bacillus subtilis metabolismus MeSH
- bakteriální proteiny metabolismus MeSH
- spory bakteriální * genetika MeSH
- tomografie elektronová * MeSH
- transmisní elektronová mikroskopie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- bakteriální proteiny MeSH
Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
CEITEC Central European Institute of Technology Masaryk University 62500 Brno Czech Republic
School of Life Sciences University of Warwick Coventry UK
Univ Grenoble Alpes CNRS CEA EMBL ISBG F 38000 Grenoble France
Univ Grenoble Alpes CNRS CEA IBS F 38000 Grenoble France
University Grenoble Alpes CEA IRIG MEM F 38054 Grenoble France
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Setlow, P. & Christie, G. New thoughts on an old topic: secrets of bacterial spore resistance slowly being revealed. Microbiol. Mol. Biol. Rev.10.1128/mmbr.00080-22 (2023). PubMed PMC
Tan IS, Ramamurthi KS. Spore formation in Bacillus subtilis. Environ. Microbiol. Rep. 2014;6:212–225. doi: 10.1111/1758-2229.12130. PubMed DOI PMC
Hilbert DW, Piggot PJ. Compartmentalization of gene expression during Bacillus subtilis spore formation. Microbiol. Mol. Biol. Rev. 2004;68:234–262. doi: 10.1128/MMBR.68.2.234-262.2004. PubMed DOI PMC
Chan H, Mohamed AMT, Grainge I, Rodrigues CDA. FtsK and SpoIIIE, coordinators of chromosome segregation and envelope remodeling in bacteria. Trends Microbiol. 2022;30:480–494. doi: 10.1016/j.tim.2021.10.002. PubMed DOI
Khanna, K. et al. The molecular architecture of engulfment during Bacillus subtilis sporulation. eLife8, e45257 (2019). PubMed PMC
Khanna K, Lopez-Garrido J, Pogliano K. Shaping an endospore: architectural transformations during Bacillus subtilis sporulation. Annu. Rev. Microbiol. 2020;74:361–386. doi: 10.1146/annurev-micro-022520-074650. PubMed DOI PMC
Morlot C, Uehara T, Marquis KA, Bernhardt TG, Rudner DZ. A highly coordinated cell wall degradation machine governs spore morphogenesis in Bacillus subtilis. Genes Dev. 2010;24:411–422. doi: 10.1101/gad.1878110. PubMed DOI PMC
Morlot C, Rodrigues CDA. The new kid on the block: a specialized secretion system during bacterial sporulation. Trends Microbiol. 2018;26:663–676. doi: 10.1016/j.tim.2018.01.001. PubMed DOI
Driks, A. & Eichenberger, P. The spore coat. Microbiol. Spectr. 10.1128/microbiolspec.tbs-0023-2016 (2016). PubMed
Popham, D. L. & Bernhards, C. B. Spore peptidoglycan. Microbiol. Spectr.10.1128/microbiolspec.tbs-0005-2012 (2015). PubMed
McKenney PT, Driks A, Eichenberger P. The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nat. Rev. Microbiol. 2013;11:33–44. doi: 10.1038/nrmicro2921. PubMed DOI PMC
Frenkiel-Krispin D, Minsky A. Nucleoid organization and the maintenance of DNA integrity in E. coli, B. subtilis and D. radiodurans. J. Struct. Biol. 2006;156:311–319. doi: 10.1016/j.jsb.2006.05.014. PubMed DOI
Asano S, Engel BD, Baumeister W. In situ cryo-electron tomography: a post-reductionist approach to structural biology. J. Mol. Biol. 2016;428:332–343. doi: 10.1016/j.jmb.2015.09.030. PubMed DOI
Liedtke J, Depelteau JS, Briegel A. How advances in cryo-electron tomography have contributed to our current view of bacterial cell biology. J. Struct. Biol. X. 2022;6:100065. PubMed PMC
Rigort A, Villa E, Bäuerlein FJB, Engel BD, Plitzko JM. Integrative approaches for cellular cryo-electron tomography: correlative imaging and focused ion beam micromachining. Methods Cell Biol. 2012;111:259–281. doi: 10.1016/B978-0-12-416026-2.00014-5. PubMed DOI
Wagner FR, et al. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat. Protoc. 2020;15:2041–2070. doi: 10.1038/s41596-020-0320-x. PubMed DOI PMC
Bauer T, Little S, Stöver AG, Driks A. Functional regions of the Bacillus subtilis spore coat morphogenetic protein CotE. J. Bacteriol. 1999;181:7043–7051. doi: 10.1128/JB.181.22.7043-7051.1999. PubMed DOI PMC
McKenney PT, Eichenberger P. Dynamics of spore coat morphogenesis in Bacillus subtilis. Mol. Microbiol. 2012;83:245–260. doi: 10.1111/j.1365-2958.2011.07936.x. PubMed DOI PMC
Tocheva EI, et al. Peptidoglycan transformations during Bacillus subtilis sporulation. Mol. Microbiol. 2013;88:673–686. doi: 10.1111/mmi.12201. PubMed DOI PMC
Castaing J-P, Nagy A, Anantharaman V, Aravind L, Ramamurthi KS. ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein. Proc. Natl Acad. Sci. USA. 2013;110:E151–E160. doi: 10.1073/pnas.1210554110. PubMed DOI PMC
Ramamurthi KS, Clapham KR, Losick R. Peptide anchoring spore coat assembly to the outer forespore membrane in Bacillus subtilis. Mol. Microbiol. 2006;62:1547–1557. doi: 10.1111/j.1365-2958.2006.05468.x. PubMed DOI
Aronson AI, Ekanayake L, Fitz-James PC. Protein filaments may initiate the assembly of the Bacillus subtilis spore coat. Biochimie. 1992;74:661–667. doi: 10.1016/0300-9084(92)90138-5. PubMed DOI
Zheng LB, Donovan WP, Fitz-James PC, Losick R. Gene encoding a morphogenic protein required in the assembly of the outer coat of the Bacillus subtilis endospore. Genes Dev. 1988;2:1047–1054. doi: 10.1101/gad.2.8.1047. PubMed DOI
Setlow P. I will survive: DNA protection in bacterial spores. Trends Microbiol. 2007;15:172–180. doi: 10.1016/j.tim.2007.02.004. PubMed DOI
Frenkiel-Krispin D, et al. Structure of the DNA-SspC complex: implications for DNA packaging, protection, and repair in bacterial spores. J. Bacteriol. 2004;186:3525–3530. doi: 10.1128/JB.186.11.3525-3530.2004. PubMed DOI PMC
Ragkousi K, Cowan AE, Ross MA, Setlow P. Analysis of nucleoid morphology during germination and outgrowth of spores of Bacillus species. J. Bacteriol. 2000;182:5556–5562. doi: 10.1128/JB.182.19.5556-5562.2000. PubMed DOI PMC
Dittmann C, Han H-M, Grabenbauer M, Laue M. Dormant Bacillus spores protect their DNA in crystalline nucleoids against environmental stress. J. Struct. Biol. 2015;191:156–164. doi: 10.1016/j.jsb.2015.06.019. PubMed DOI
Doan T, et al. Novel secretion apparatus maintains spore integrity and developmental gene expression in Bacillus subtilis. PLoS Genet. 2009;5:e1000566. doi: 10.1371/journal.pgen.1000566. PubMed DOI PMC
Peluso EA, Updegrove TB, Chen J, Shroff H, Ramamurthi KS. A 2-dimensional ratchet model describes assembly initiation of a specialized bacterial cell surface. Proc. Natl Acad. Sci. USA. 2019;116:21789–21799. doi: 10.1073/pnas.1907397116. PubMed DOI PMC
Driks A, Roels S, Beall B, Moran CP, Losick R. Subcellular localization of proteins involved in the assembly of the spore coat of Bacillus subtilis. Genes Dev. 1994;8:234–244. doi: 10.1101/gad.8.2.234. PubMed DOI
Müllerová D, Krajčíková D, Barák I. Interactions between Bacillus subtilis early spore coat morphogenetic proteins. FEMS Microbiol. Lett. 2009;299:74–85. doi: 10.1111/j.1574-6968.2009.01737.x. PubMed DOI
Delerue T, et al. Bacterial developmental checkpoint that directly monitors cell surface morphogenesis. Dev. Cell. 2022;57:344–360.e6. doi: 10.1016/j.devcel.2021.12.021. PubMed DOI PMC
Wang KH, et al. The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis. Mol. Microbiol. 2009;74:634–649. doi: 10.1111/j.1365-2958.2009.06886.x. PubMed DOI PMC
de Francesco M, et al. Physical interaction between coat morphogenetic proteins SpoVID and CotE is necessary for spore encasement in Bacillus subtilis. J. Bacteriol. 2012;194:4941–4950. doi: 10.1128/JB.00914-12. PubMed DOI PMC
Costa T, Isidro AL, Moran CP, Henriques AO. Interaction between coat morphogenetic proteins SafA and SpoVID. J. Bacteriol. 2006;188:7731–7741. doi: 10.1128/JB.00761-06. PubMed DOI PMC
Nunes F, et al. SpoVID functions as a non-competitive hub that connects the modules for assembly of the inner and outer spore coat layers in Bacillus subtilis. Mol. Microbiol. 2018;110:576–595. doi: 10.1111/mmi.14116. PubMed DOI PMC
Pereira FC, et al. A LysM domain intervenes in sequential protein-protein and protein-peptidoglycan interactions important for spore coat assembly in Bacillus subtilis. J. Bacteriol. 2019;201:e00642–18. doi: 10.1128/JB.00642-18. PubMed DOI PMC
Ozin AJ, Samford CS, Henriques AO, Moran CP. SpoVID guides SafA to the spore coat in Bacillus subtilis. J. Bacteriol. 2001;183:3041–3049. doi: 10.1128/JB.183.10.3041-3049.2001. PubMed DOI PMC
Krajcíková D, Lukácová M, Müllerová D, Cutting SM, Barák I. Searching for protein-protein interactions within the Bacillus subtilis spore coat. J. Bacteriol. 2009;191:3212–3219. doi: 10.1128/JB.01807-08. PubMed DOI PMC
Harwood, C. R. & Cutting, S. M. Molecular Biological Methods for Bacillus (Wiley, 1990).
Wolff G, et al. Mind the gap: micro-expansion joints drastically decrease the bending of FIB-milled cryo-lamellae. J. Struct. Biol. 2019;208:107389. doi: 10.1016/j.jsb.2019.09.006. PubMed DOI
Moravcová, J., Pinkas, M., Holbová, R. & Nováček, J. Preparation and Cryo-FIB micromachining of saccharomyces cerevisiae for cryo-electron tomography. J. Vis. Exp.10.3791/62351 (2021). PubMed
Kandiah E, et al. CM01: a facility for cryo-electron microscopy at the European Synchrotron. Acta Crystallogr. Sect. Struct. Biol. 2019;75:528–535. doi: 10.1107/S2059798319006880. PubMed DOI PMC
Turoňová B, et al. Benchmarking tomographic acquisition schemes for high-resolution structural biology. Nat. Commun. 2020;11:876. doi: 10.1038/s41467-020-14535-2. PubMed DOI PMC
Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 2005;152:36–51. doi: 10.1016/j.jsb.2005.07.007. PubMed DOI
Zheng SQ, et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods. 2017;14:331–332. doi: 10.1038/nmeth.4193. PubMed DOI PMC
Mastronarde DN. Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package. J. Microsc. 2008;230:212–217. doi: 10.1111/j.1365-2818.2008.01977.x. PubMed DOI
Zheng S, et al. AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. J. Struct. Biol. X. 2022;6:100068. PubMed PMC
Chen M, et al. Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods. 2017;14:983–985. doi: 10.1038/nmeth.4405. PubMed DOI PMC
Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996;116:71–76. doi: 10.1006/jsbi.1996.0013. PubMed DOI
Goddard TD, et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. Publ. Protein Soc. 2018;27:14–25. doi: 10.1002/pro.3235. PubMed DOI PMC